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Idea #9044
open[Crunch2] [Workbench] Browse and show tools using the GA4GH tool registry API
Start date:
Due date:
Story points:
-
Release:
Release relationship:
Auto
Description
This first version will just allow users to browse/select public workflows that have been registered at dockstore.org.
The API endpoint should be configurable, though, so that when Arvados supports the tool registry API itself (#9042) users will be able to select tools that are registered in Arvados.
Related issues
Updated by Tom Clegg over 8 years ago
- Description updated (diff)
- Category set to Workbench
Updated by Brett Smith over 8 years ago
- Target version deleted (
2016-07-20 sprint)
Updated by Brett Smith about 8 years ago
- Assigned To set to Radhika Chippada
Radhika's for grooming.
Updated by Brett Smith about 8 years ago
- Subject changed from [Crunch2] [Workbench] Browse and show tools using the tool registry API to [Crunch2] [Workbench] Browse and show tools using the GA4GH tool registry API
Updated by Tom Morris about 8 years ago
- Target version set to Arvados Future Sprints
Updated by Radhika Chippada about 8 years ago
tom (on irc):
2:02 https://github.com/ga4gh/tool-registry-schemas
2:02 http://editor.swagger.io/#/?import=https://raw.githubusercontent.com/ga4gh/tool-registry-schemas/develop/src/main/resources/swagger/ga4gh-tool-discovery.yaml
2:02 https://www.dockstore.org:8443/api/v1/tools
2:02 curl https://www.dockstore.org:8443/api/v1/tools | jq .
Updated by Radhika Chippada about 8 years ago
Implementation:
- Add a “Run a tool” button in the panel header next to “Run a pipeline” in dashboard.
- Add a config parameter to workbench to configure the tool registry end-point
- When this button is pressed, present a “Choose a tool to run” modal similar to “Choose a pipeline to run” to the user
- Get the tool json from the configured end point (do we want to cache this and pull at regular intervals or for each click?)
- Present each version of each tool from the json as a separate link in the popup
pcawg-merge-annotate - master pcawg-merge-annotate - 1.0.0 …
- When a link from the popup is clicked on, show the tool detail in preview pane on the right
- When OK button is selected, create a CR with the selection as mount(s) and take the user to the CR page
- The CR created for the selected tool version will have:
- Name = tool - version (ex: pcawg-merge-annotate - master)
- use mount kind json to store the selection
- store the entire selected tool record including all version as mount point “/var/lib/cwl/tool”
- store the selected tool version as mount “/var/lib/cwl/tool_version”
Out of scope for this story:
- Support for json mount kind
- Presenting appropriate input selection options based on the selected tool description
- Running the selected tool
Updated by Tom Morris about 8 years ago
- Target version deleted (
Arvados Future Sprints)
Updated by Peter Amstutz over 1 year ago
- Target version set to Future
- Assigned To deleted (
Radhika Chippada) - Category changed from Workbench to Workbench2
Updated by Peter Amstutz over 1 year ago
- Release set to 60
- Target version deleted (
Future)
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